A Study On The Modeling,molecular Docking And Interactions Of The SoxAX In Thiobacillus Denitrificans

Thiobacillus denitrificans is a type of sulfur oxidizing bacteria?SOB?,also known as an obligately chemolithoautotrophic facultatively anaerobeic bacterium.I t was famous for its high desulfurization efficiency and formed sulfur globule,as well as oxidizing sulfur compound with dinitrifide pathway under anaerobic conditions.It was widely used on biological desulfurization denitrification process,sewage treatment,metal anti-corrosion technology,petrochemicals and other applications.Sox system encoded by the the sox?sulfur oxidizing?gene cluster,is one of the most widely distributed sulfur oxidation pathways in sulfur-oxidizing bacterium,and it is important to the growth of bacterium and biogeochemical sulfur cycle.But there is still not having the structures of Sox protein of Thiobacillus denitrificans in PDB database.We have successfully built SoxA and SoxX protein by threading modeling with i-TASSER sever,and successfully constructed stable heme-binding Sox AX dimer of Thiobacillus denitrificans,after superimpose dimer crystal structure?1H32?and optimizated structure by energy minimization and moleculer dynamics on Discovery Studio 3.5.After that,we are making enzyme-substrate docking study bewteen Sox AX and thiosulfate,sulfite and hydrogen sulfide?Three methods,PROCHECK,VERIFY₃D and PROSA,were using for evaluating the rationality of our modeling by computing the Dihedral angle and potential energy.All evidences were showed that we have constructed a reasonable structure for Sox AX,which is the basic model for further on interaction energy analysis and enzyme-ligand docking.,With interaction energy analysis,we found out that hydrogen bond is the major interaction force for Sox AX dimer.,and there are 8 hydrogen bonds formed between Sox A and SoxX.Interaction energy shows that electrostatic interaction is the major force drived for SoxAX dimer binding.Four residues on Sox A?ARG160,GLN174,ARG179,ARG219?and six residues on SoxX?GLY18,THR35,MET37?PRO67?SER68?THR69?played important roles on SoxAX interaction.We are using molecular docking tools to study potential active site of Thiobacillus denitrificans SoxAX dimer?Td SoxAX?and Rhodovulum Sulfidophilum SoxAX dimer?Rs SoxAX?which combined with different sulfur compounds.The result shows that the size of active sphere and insolved residues.have been successfully predicted.Docking analysis shows that hydrogen bonds are the matains a major role on substrate binding.ARG210,CYS214,GLU183,GLN217 and heme on SoxA submit are possible substrate binding area of Thiobacillus denitrificans.